NMDS for Reference streams-10% removed
16 July, 2021
R version 4.0.3 (2020-10-10) – “Bunny-Wunnies Freak Out”
Packages used for NMDS: vegan (version 2.5-7)
Methods
The document serves as an example of analyses that will be conducted to identify natural variations in benthic communities across Virginia. These NMDS will support the Genus level IBI development process. This analysis is the first run of all of reference sites in Virginia. No West Virginia DEP data is used in this analysis. Several reference sites have been sent back to Virginia DEQ biologists for one more review.
The dataset used is a subset of reference stations collected in Virginia. If stations appeared in the dataset more than 4 times, then the most recent 4 samples were used and the rest removed. Taxa that occurred in the dataset < 10% of the time were removed. The data was log10 +1 transformed. Environmental factors were compiled for each station and used to plot over the NMDS to show environmental variation associated with the community matrix. The envfit function in Vegan was used to plot the continuous environmental variables.
The first step was to read in the reference site bug taxa list and environmental factors dataset for each station. Join the environmental dataset with the bug dataset to account for multiple observations of each station and collection date and time.
Check to make sure the bug and environmental join was successful:
Number of rows in Community Matrix: 854
Number or rows in Environmental Matrix: 858
The data was log10+1 transformed. Rare taxa (<=10%) were removed.
Run NMDS for reference communities
## Run 0 stress 0.1684074
## Run 1 stress 0.1685779
## ... Procrustes: rmse 0.003267809 max resid 0.07093681
## Run 2 stress 0.1684073
## ... New best solution
## ... Procrustes: rmse 0.0001266153 max resid 0.002595457
## ... Similar to previous best
## Run 3 stress 0.1694493
## Run 4 stress 0.1687056
## ... Procrustes: rmse 0.00336004 max resid 0.07511734
## Run 5 stress 0.1685908
## ... Procrustes: rmse 0.002140328 max resid 0.06192395
## Run 6 stress 0.1686516
## ... Procrustes: rmse 0.002420567 max resid 0.06191808
## Run 7 stress 0.1684666
## ... Procrustes: rmse 0.001172967 max resid 0.0330259
## Run 8 stress 0.1685785
## ... Procrustes: rmse 0.003736797 max resid 0.07435475
## Run 9 stress 0.1687616
## ... Procrustes: rmse 0.004266263 max resid 0.07264733
## Run 10 stress 0.1685902
## ... Procrustes: rmse 0.002139672 max resid 0.06194481
## Run 11 stress 0.1687013
## ... Procrustes: rmse 0.004134911 max resid 0.07368102
## Run 12 stress 0.1683998
## ... New best solution
## ... Procrustes: rmse 0.00245399 max resid 0.07099414
## Run 13 stress 0.1686374
## ... Procrustes: rmse 0.002434842 max resid 0.06176666
## Run 14 stress 0.168519
## ... Procrustes: rmse 0.002543314 max resid 0.0737268
## Run 15 stress 0.1685776
## ... Procrustes: rmse 0.002132679 max resid 0.06176917
## Run 16 stress 0.1685912
## ... Procrustes: rmse 0.003247928 max resid 0.07120008
## Run 17 stress 0.1685785
## ... Procrustes: rmse 0.003628517 max resid 0.07125442
## Run 18 stress 0.1684073
## ... Procrustes: rmse 0.00245374 max resid 0.07099415
## Run 19 stress 0.1685178
## ... Procrustes: rmse 0.00361 max resid 0.0767033
## Run 20 stress 0.1685776
## ... Procrustes: rmse 0.002137212 max resid 0.06179338
## Run 21 stress 0.1695664
## Run 22 stress 0.1694941
## Run 23 stress 0.1687015
## ... Procrustes: rmse 0.003358745 max resid 0.07518244
## Run 24 stress 0.1685774
## ... Procrustes: rmse 0.003783563 max resid 0.07639676
## Run 25 stress 0.1696084
## Run 26 stress 0.1685773
## ... Procrustes: rmse 0.00213494 max resid 0.06176447
## Run 27 stress 0.1684077
## ... Procrustes: rmse 0.002456996 max resid 0.0710458
## Run 28 stress 0.1684075
## ... Procrustes: rmse 0.002453015 max resid 0.07097477
## Run 29 stress 0.1696052
## Run 30 stress 0.168407
## ... Procrustes: rmse 0.002451901 max resid 0.07099345
## Run 31 stress 0.168637
## ... Procrustes: rmse 0.002428719 max resid 0.06177029
## Run 32 stress 0.1687438
## ... Procrustes: rmse 0.003274938 max resid 0.07480915
## Run 33 stress 0.1694864
## Run 34 stress 0.1684581
## ... Procrustes: rmse 0.001195828 max resid 0.03324885
## Run 35 stress 0.1686511
## ... Procrustes: rmse 0.003441384 max resid 0.07110878
## Run 36 stress 0.1687412
## ... Procrustes: rmse 0.004113679 max resid 0.07639219
## Run 37 stress 0.1684821
## ... Procrustes: rmse 0.00275688 max resid 0.07083849
## Run 38 stress 0.1685773
## ... Procrustes: rmse 0.00376374 max resid 0.07567305
## Run 39 stress 0.1685907
## ... Procrustes: rmse 0.003244964 max resid 0.07116412
## Run 40 stress 0.1687676
## ... Procrustes: rmse 0.004319747 max resid 0.07585751
## Run 41 stress 0.1684656
## ... Procrustes: rmse 0.002715933 max resid 0.07085339
## Run 42 stress 0.1685902
## ... Procrustes: rmse 0.003242766 max resid 0.07115944
## Run 43 stress 0.1686395
## ... Procrustes: rmse 0.002090333 max resid 0.04484982
## Run 44 stress 0.1687612
## ... Procrustes: rmse 0.003495713 max resid 0.07337875
## Run 45 stress 0.1687013
## ... Procrustes: rmse 0.003326373 max resid 0.07395997
## Run 46 stress 0.1685778
## ... Procrustes: rmse 0.00213211 max resid 0.06177182
## Run 47 stress 0.1684074
## ... Procrustes: rmse 0.002451144 max resid 0.07098344
## Run 48 stress 0.1684001
## ... Procrustes: rmse 0.0001359149 max resid 0.002198067
## ... Similar to previous best
## *** Solution reached##
## Call:
## metaMDS(comm = NMDSten[, 6:83], k = 3, trymax = 1000)
##
## global Multidimensional Scaling using monoMDS
##
## Data: NMDSten[, 6:83]
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1683998
## Stress type 1, weak ties
## Two convergent solutions found after 48 tries
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'NMDSten[, 6:83]'
Envfit results from Vegan package :
##
## ***VECTORS
##
## NMDS1 NMDS2 r2 Pr(>r)
## JulianDate -0.54082 0.84114 0.0745 0.658
## Latitude 0.87395 -0.48602 0.2561 0.192
## Longitude 0.98919 0.14663 0.2643 0.189
## US_L3CODE -0.13768 -0.99048 0.2884 0.146
## Order -0.96417 -0.26530 0.7460 0.002 **
## EDASOrder -0.96417 -0.26530 0.7460 0.002 **
## totalArea_sqMile -0.72068 -0.69327 0.4557 0.049 *
## ELEVMEAN -0.89598 -0.44410 0.5281 0.013 *
## SLPMEAN -0.42780 -0.90387 0.7659 0.002 **
## wshdRain_mmyr -0.70382 -0.71037 0.4590 0.049 *
## siteRain_mmyr -0.65103 0.75905 0.2733 0.182
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2
## SeasonFall -0.5647 0.6258
## SeasonOutside Sample Window -0.5792 0.1746
## SeasonSpring -0.5968 0.3210
## GradientMACS -0.5818 0.4412
## CoastalTRUE -0.5818 0.4412
## US_L3NAMEMiddle Atlantic Coastal Plain -0.5219 0.6919
## US_L3NAMESoutheastern Plains -0.6151 0.3019
## US_L4NAMEChesapeake-Pamlico Lowlands and Tidal Marshes -0.5791 0.3916
## US_L4NAMEMid-Atlantic Flatwoods -0.4837 0.8921
## US_L4NAMERolling Coastal Plain -0.6151 0.3019
## ASSESS_REGPRO -0.6086 0.3182
## ASSESS_REGTRO -0.4837 0.8921
## TidalN -0.5823 0.4494
## TidalT -0.5791 0.3916
## VAHUSBCB -0.5022 0.5568
## VAHUSBCU -0.6093 0.5686
## VAHUSBYO -0.6202 0.1344
## BasinChes. Bay and Small Coastal Basin -0.5022 0.5568
## BasinChowan and Dismal Swamp River Basin -0.6093 0.5686
## BasinYork River Basin -0.6202 0.1344
## Basin_CodeChowan-Dismal -0.6093 0.5686
## Basin_CodeSmall Coastal -0.5022 0.5568
## Basin_CodeYork -0.6202 0.1344
## CountyCityNameCaroline -0.6891 0.0814
## CountyCityNameDinwiddie -0.7258 0.4332
## CountyCityNameHanover -0.5513 0.1875
## CountyCityNameKing and Queen -0.4252 0.7219
## CountyCityNameNorthumberland -0.5791 0.3916
## CountyCityNameSouthampton -0.4837 0.8921
## CountyCityNameSussex -0.7531 -0.1309
## WQS_CLASSIII -0.6579 0.1630
## WQS_CLASSVII -0.5395 0.5957
## WQS_SPSTDS -0.5769 0.3975
## WQS_SPSTDSNEW-21 -0.6455 1.0095
## WQS_PWS -0.5818 0.4412
## WQS_TROUT -0.5818 0.4412
## WQS_TIER_III -0.5818 0.4412
##
## Goodness of fit:
## r2 Pr(>r)
## Season 0.1958 0.341
## Gradient 0.0000 1.000
## Coastal 0.0000 1.000
## US_L3NAME 0.2663 0.075 .
## US_L4NAME 0.4267 0.043 *
## ASSESS_REG 0.4189 0.017 *
## Tidal 0.0030 0.978
## VAHUSB 0.2901 0.148
## Basin 0.2901 0.148
## Basin_Code 0.2901 0.148
## CountyCityName 0.8557 0.010 **
## WQS_CLASS 0.3332 0.034 *
## WQS_SPSTDS 0.1814 0.133
## WQS_PWS 0.0000 1.000
## WQS_TROUT 0.0000 1.000
## WQS_TIER_III 0.0000 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999
##
## 840 observations deleted due to missingnessPlot with Station IDs
Plot with Axis 3
Plot with Species
Season
##
## Call:
## mrpp(dat = bugsnms[, 6:83], grouping = samplescoresenv$Season, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Fall Outside Sample Window Spring
## delta 0.6419 0.6564 0.6475
## n 414 13 427
##
## Chance corrected within-group agreement A: 0.03778
## Based on observed delta 0.6449 and expected delta 0.6702
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Season with continuous variable vectors
Ecoregion
##
## Call:
## mrpp(dat = bugsnms[, 6:83], grouping = samplescoresenv$US_L3NAME, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Blue Ridge Central Appalachians Middle Atlantic Coastal Plain
## delta 0.5768 0.5884 0.507
## n 154 40 25
## Northern Piedmont Piedmont Ridge and Valley Southeastern Plains
## delta 0.6265 0.5919 0.6382 0.5931
## n 101 138 259 137
##
## Chance corrected within-group agreement A: 0.09754
## Based on observed delta 0.6049 and expected delta 0.6702
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Basin
##
## Call:
## mrpp(dat = bugsnms[, 6:83], grouping = samplescoresenv$Basin_Code, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Appomattox Chowan-Dismal James-Lower James-Middle James-Upper New
## delta 0.5512 0.6223 0.5695 0.5932 0.6337 0.6312
## n 15 33 36 61 120 78
## Potomac-Lower Potomac-Shenandoah Rappahannock Roanoke Small Coastal
## delta 0.6619 0.6423 0.648 0.5886 0.528
## n 31 42 144 87 21
## Tennessee-Big Sandy Tennessee-Clinch Tennessee-Holston Yadkin York
## delta 0.5827 0.6114 0.6064 0.5361 0.6313
## n 16 50 53 4 63
##
## Chance corrected within-group agreement A: 0.07782
## Based on observed delta 0.6181 and expected delta 0.6702
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Admin Region
##
## Call:
## mrpp(dat = bugsnms[, 6:83], grouping = samplescoresenv$ASSESS_REG, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## BRRO NRO PRO SWRO TRO VRO
## delta 0.6224 0.6706 0.5961 0.6149 0.4894 0.6291
## n 250 195 122 156 21 110
##
## Chance corrected within-group agreement A: 0.06618
## Based on observed delta 0.6259 and expected delta 0.6702
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Sample Method
##
## Call:
## mrpp(dat = bugsnms[, 6:83], grouping = samplescoresenv$Gradient, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MACS Riffle
## delta 0.5978 0.637
## n 163 691
##
## Chance corrected within-group agreement A: 0.06075
## Based on observed delta 0.6295 and expected delta 0.6702
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999BioRegion- Not in dataset
Stream Order
##
## Call:
## mrpp(dat = bugsnms[, 6:83], grouping = samplescoresenv$Order, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## 1 2 3 4 5 6
## delta 0.6472 0.6598 0.6353 0.6293 0.592 0.4265
## n 277 248 172 114 41 2
##
## Chance corrected within-group agreement A: 0.0408
## Based on observed delta 0.6429 and expected delta 0.6702
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Water Quality Standard Class
##
## Call:
## mrpp(dat = bugsnms[, 6:83], grouping = samplescoresenv$WQS_CLASS, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## III IV V VI VII
## delta 0.6603 0.6257 0.6159 0.5843 0.5843
## n 331 185 87 209 42
##
## Chance corrected within-group agreement A: 0.06609
## Based on observed delta 0.6259 and expected delta 0.6702
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Natural Trout Water WQS?
